Comparison of different samples for 2019 novel coronavirus detection by nucleic acid amplification tests

Xie, Chunbao; Jiang, Lingxi; Huang, Guo; Pu, Hong; Gong, Bo; He, Lin; Ma, Shanshan; Chen, Xuemei; Long, Bo; Guo, Shuang; Yu, Hua; Jiang, Li; Yang, Xiangdong; Shi, Yi; Yang, Zhenglin

doi:10.1016/j.ijid.2020.02.050

Cited by 324 publications

(355 citation statements)

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“…In this model, the probability of RT-PCR assays to detect one copy of SARS-CoV-2 is only 26%. This finding may explain, at least in part, the low reported 47-56% detection rates of SARS-CoV-2 in positive samples by RT-PCR 17,22 . We further found that the LOD appears to be independent of the virus genome size.…”

Section: Mathematical Model Of Rt-pcrmentioning

confidence: 94%

“…Currently, RT-PCR is considered the gold standard of diagnosis for SARS-CoV-2 due to its ease of use and high sensitivity. RT-PCR has been reported to detect SARS-CoV-2 in saliva 15 , pharyngeal swab, blood, anal swab 16 , urine, stool 17 , and sputum specimens 18 . In laboratory conditions, the RT-PCR methodology has been shown to detect 4-8 copies of virus, through amplification of targets in the Orf1ab, E and N viral genes, at 95% confidence intervals [19][20][21] .…”

Section: Introductionmentioning

confidence: 99%

“…In laboratory conditions, the RT-PCR methodology has been shown to detect 4-8 copies of virus, through amplification of targets in the Orf1ab, E and N viral genes, at 95% confidence intervals [19][20][21] . However, only about 47-59% of the positive cases were identified by RT-PCR, and 75% of RT-PCR negative results were actually found to be positive, with repeated tests required 17,[22][23][24] . In addition, there is evidence suggesting that heat inactivation of clinical samples causes loss of virus particles, thereby hindering the efficiency of downstream diagnostic evaluation 25 .…”

Section: Introductionmentioning

confidence: 99%

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Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing

Debruyne

Spencer

et al. 2020

Preprint

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Many detection methods have been used or reported for the diagnosis and/or surveillance of SARS-CoV-2. Among them, reverse transcription polymerase chain reaction (RT-PCR) is the most sensitive, claiming detection of about 5 copies of viruses. However, it has been reported that only 47-59% of the positive cases were identified by RT-PCR, probably due to loss or degradation of virus RNA in the sampling process, or even mutation of the virus genome. Therefore, developing highly sensitive methods is imperative to ensure robust detection capabilities. With the goal of improving sensitivity and accommodate various application settings, we developed a multiplex-PCR-based method comprised of 172 pairs of specific primers, and demonstrated its efficiency to detect SARS-CoV-2 at low copy numbers. The assay produced clean characteristic target peaks of defined sizes, which allowed for direct identification of positives by electrophoresis. In addition, optional sequencing can provide further confirmation as well as phylogenetic information of the identified virus(es) for specific strain discrimination, which will be of paramount importance for surveillance purposes that represent a global health imperative. Finally, we also developed in parallel a multiplex-PCR-based metagenomic method that is amenable to detect SARS-CoV-2, with the additional benefit of its potential for uncovering mutational diversity and novel pathogens at low sequencing depth.

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Section: Mathematical Model Of Rt-pcrmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing

Debruyne

Spencer

et al. 2020

Preprint

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“…Anorexia, Chills, Shortness of breath, dyspnea, chest pain, confusion, and nausea/vomiting were reported in respectively 5, 5, 6, 5, 7, 2, and 9 studies. Overall prevalence of these symptoms was 24% (95% CI, 13-34), 19% (95% CI, [11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27], 27% (95% CI, 12-42), 31% (95% CI, 14-48), 6% (95% CI, 2-9), 1% (95% CI, 0-2) and 6% (95% CI, 3-8) (Supplementary File and Table 2).…”

Section: Clinical Findingsmentioning

confidence: 99%

Clinical and Paraclinical Characteristics of COVID-19 patients: A systematic review and meta-analysis

Heydari

Rismantab

Shamshirian

et al. 2020

Preprint

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Introduction:Recently, a new strain of coronaviruses, which originated from Wuhan City, Hubei Province, China has been identified. According to the high prevalence of new coronavirus, further investigation on the clinical and paraclinical features of this disease seems essential. Hence, we carried out this systematic review and meta-analysis to figure out the unknown features. Methods:This study was performed using databases of Web of Science, Scopus and PubMed.We considered English cross-sectional and case-series papers which reported clinical, radiological, and laboratory characteristics of patients with COVID-19. We used STATA v.11 and random effect model for data analysis. Results:In the present meta-analysis, 32 papers including 49504 COVID-19 patients were studied.The most common clinical symptoms were fever (84%), cough (65%) and fatigue (42%), respectively. The most common radiological and paraclinical features were bilateral pneumonia (61%), ground-glass opacity (50%), thrombocytopenia (36%) and lymphocytopenia (34%). The study also showed that the frequency of comorbidities and early symptoms was higher in critically severe patients. Moreover, we found the overall mortality rate of three percent.Conclusion: According to that there are many cases without Computed Tomography Scan findings or clear clinical symptoms, it is recommended to use other confirming methods such RNA sequencing in order to identification of suspicious undiagnosed patients. Moreover, while there is no access to clinical and paraclinical facilities in in public places such as airports and border crossings, it is recommended to consider factors such as fever, cough, sputum and fatigue.

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“…Diese ist bei medizinischen Maßnahmen und Operationen im Nasen-Rachen-Raum und Kopf-Hals-Bereich besonders hoch. Erste Studien deuten auf einen niedrigen oder ausbleibenden Nachweis von SARS-CoV-2 im Urin und Blut von an COVID-19 erkrankten Patienten hin, wohingegen das Virus im Stuhl hochfrequent nachweisbar war [8,9]. Weiterhin sollte auch ein besonderes Augenmerk auf laparoskopischen Eingriffen liegen, für die Studien eine Virusdissemination durch das Pneumoperitoneum beschrieben haben [10,11].…”

Section: Interventionen Und Operationen An Sars-cov-2-positiven Patieunclassified

Urologie in der Corona-Virus-Pandemie – Leitfaden 4/20

Kriegmair

Kowalewski

Lange

et al. 2020

Urologe

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Comparison of different samples for 2019 novel coronavirus detection by nucleic acid amplification tests

Abstract: A severe respiratory ongoing outbreak of pneumonia associated with 2019 novel coronavirus was recently emerged in China. Here, we reported the epidemiological, clinical, laboratory and radiological characteristics of 19 suspect cases. We compared J o u r n a l P r e -p r o o f

Cited by 324 publications

References 10 publications

Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing

Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing

Clinical and Paraclinical Characteristics of COVID-19 patients: A systematic review and meta-analysis

Urologie in der Corona-Virus-Pandemie – Leitfaden 4/20

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